normalizeSCP {scp} | R Documentation

## Normalize single-cell proteomics (SCP) data

### Description

This function normalises an assay in a `QFeatures` according to the supplied method (see Details). The normalized data is added as a new assay

### Usage

    normalizeSCP(object, i, name = "normAssay", method, ...)

### Arguments

`object` | An object of class `QFeatures`.
`i` | A numeric vector or a character vector giving the index or the name, respectively, of the assay(s) to be processed.
`name` | A `character(1)` naming the new assay name. Defaults is are `normAssay`.
`method` | `character(1)` defining the normalisation method to apply. See Details.'
`...` | Additional parameters passed to `MsCoreUtils::normalizeMethods()`.

### Details

The `method` parameter in `normalize` can be one of `"sum"`, `"max"`, `"center.mean"`, `"center.median"`, `"div.mean"`, `"div.median"`, `"diff.meda"`, `"quantiles`", `"quantiles.robust`" or `"vsn"`. The `MsCoreUtils::normalizeMethods()` function returns a vector of available normalisation methods.

- For `"sum"` and `"max"`, each feature's intensity is divided by the maximum or the sum of the feature respectively. These two methods are applied along the features (rows).

- `"center.mean"` and `"center.median"` center the respective sample (column) intensities by subtracting the respective column means or medians. `"div.mean"` and `"div.median"` divide by the column means or medians. These are equivalent to `sweep`ing the column means (medians) along `MARGIN = 2` with `FUN = "-"` (for `"center.*"`) or `FUN = "/"` (for `"div.*"`).

- `"diff.median"` centers all samples (columns) so that they all match the grand median by subtracting the respective columns medians differences to the grand median.

- Using `"quantiles"` or `"quantiles.robust"` applies (robust) quantile normalisation, as implemented in `preprocessCore::normalize.quantiles()` and `preprocessCore::normalize.quantiles.robust()`. `"vsn"` uses the `vsn::vsn2()` function. Note that the latter also glog-transforms the intensities. See respective manuals for more details and function arguments.

For further details and examples about normalisation, see `MsCoreUtils::normalize_matrix()`.

### Value

A `QFeatures` object with an additional assay containing the normalized data.

### See Also

QFeatures::normalize for more details about `normalize`

[Package scp version 1.4.0 Index]